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3,576 results for “rare”
A droplet digital polymerase chain reaction assay to detect rare helminth parasites infecting natural host populations (Vancouver Island 2023, University of Wisconsin Madison Laboratory colony 2024)
Helminth infections represent a significant challenge to human, livestock, and wildlife health, yet they remain relatively under-studied, especially in terms of their ecological impacts. Better understanding of how these parasites spread in wildlife populations could improve our ability to predict and manage disease transmission across various species. Traditional detection methods, such as visually identifying parasites in environmental samples or infected hosts, often fall short, especially during the early stages of infection when parasite loads are minimal. In this study, we introduce a highly sensitive and precise droplet digital PCR (ddPCR) assay that quantifies helminth DNA in aquatic habitats, focusing on the 18S rRNA gene as a marker. These data utilize the model host-parasite system between the tapeworm Schistocephalus solidus, and its cyclopoid copepod host, Acanthocyclops robustus. The molecular assays are built around creating an infection standard in the lab, where copepods were singly infected with a single tapeworm parasite. We extracted DNA from 100 infected adults and used this as a standard to translate gene copy numbers from the ddPCR reactions to actual animal values. After creating a known lab standard, we then use the generated probes and primers to detect (and quantify!) infection burdens in field samples, which include both water filter samples (eDNA) and zooplankton tows from several lakes around Vancouver Island, B.C. The data presented here include well-specific data from ddPCR runs (amplitude of individual level oil droplets in the reaction) as well as each ddPCR analysis in its entirety. In order to prove the specificity of probes and probe-primers, we include here ddPCR runs of closely related helminth species, Schistocephalus cotti and Schistocephalus pungitii. We also consider the binding to another genera of copepod, the calanoid Eurytomora. All of the data wrangling, analysis, and data visualization are included as .Rmd files in th
Data of publication Ultra-narrow Optical Linewidths in Rare-Earth Molecular Crystals
<p>Data corresponding to main text Figures, Extended Data figures, and Supplementary Figures in publication 'Ultra-narrow Optical Linewidths in Rare-Earth Molecular Crystals, by D. Serrano, S. Kumar Kuppusamy, B. Heinrich, O. Fuhr, M. Ruben and P. Goldner.</p>
Data from: Functional structure of European forest beetle communities is enhanced by rare species
<p>From article abstract:</p> <p><a href="https://doi.org/10.1016/j.biocon.2022.109491">https://doi.org/10.1016/j.biocon.2022.109491</a></p> <p><strong>ABSTRACT</strong></p> <p>Biodiverse communities have been shown to sustain high levels of multifunctionality and thus a loss of species likely negatively impacts ecosystem functions. For most taxa, however, the roles of individual species are poorly known. Rare species, often the most likely to go extinct, may have unique traits leading to unique functional roles. Alternatively, rare species may be functionally redundant, such that their loss would not disrupt ecosystem functions. We quantified the functional role of rare species by using capture records of wood-living (saproxylic) beetle species, combined with recent databases of their morphological and ecological traits, from three regions in central and northern Europe. Using a rarity index based on species’ local abundance, geographic range, and habitat breadth, we used local and regional species removal simulations to examine the contributions of both the rarest and the most common beetle species to three measures of community functional structure: functional richness, functional specialization, and functional originality. In both regional species pools and local communities, all three of these measures declined more rapidly when rare species were removed than under common (or random) species removal scenarios. These consistent patterns across scales and among several forest types give evidence that rare species provide unique functional contributions, and that their loss may disproportionately impact ecosystem functions. This implies that conservation measures targeting rare and endangered species, such as preserving intact forests with dead wood and mature trees, can provide broader ecosystem-level benefits. Experimental research linking functional structure to ecosystem processes should be prioritized to increase our understanding of the functional consequences of species loss and to develop more effective conservation strategies.</p> <p> </p> <p><strong>DATASET DESCRIPTION</strong></p> <p>This dataset includes a) beetle capture information and b) beetle trait information from three countries: 1) Norway, 2) Finland, and 3) Germany. </p> <p> </p> <p><strong>FILES</strong></p> <p><strong>readme.txt</strong> -- this has the information from this description section</p> <p><strong>Norway_traits.csv</strong>, <strong>Finland_traits.csv</strong>, <strong>Germany_traits.csv</strong> -- these are the trait files, including all species</p> <p><strong>Norway_sites.species.csv</strong>, <strong>Finland_sites.species.csv</strong>, <strong>Germany_sites.species.csv</strong> -- this has species (rows) by sites (columns); values are the number of beetles caught (for number of traps, dates, and other site covariates, see related dataset: <a href="https://doi.org/10.5061/dryad.tmpg4f50b">https://doi.org/10.5061/dryad.tmpg4f50b</a> and manuscript: <a href="https://doi.org/10.1111/jbi.14272">https://doi.org/10.1111/jbi.14272</a>). Species names follow GBIF taxonomic backbone.</p> <p><strong>Traits_METADATA.csv</strong> -- this has information on all the fields in the trait data</p> <p> </p>
Rare Disease analysis in Mondo
<p>To answer the question of 'How many rare diseases are there?' we analyzed terms in Mondo to get a total count of Rare Diseases as defined in Mondo Disease Ontology (Mondo).</p> <p> </p> <p>Methods</p> <p>This analysis was performed on the <a href="http://purl.obolibrary.org/obo/mondo/releases/2019-09-30/mondo.json">Mondo 2019-09-30 release</a>.</p> <p><strong>1. Get all 'Disease' terms from Mondo</strong></p> <p>First we get all the terms in Mondo that are a descendants of <code>MONDO:0000001 'Disease'</code>.</p> <p>There are <code>21633</code> Mondo disease terms.</p> <p><strong>2. Filter terms that are descendants of 'disease susceptibility'</strong></p> <p>We then filter out terms that are descendants of <code>MONDO:0042489 'disease susceptibility'</code>, to avoid counting ambiguous terms that are related to disease susceptibility and not the actual disease itself.</p> <p>This gives us a list of <code>21563</code> Mondo rare disease terms.</p> <p><strong>3. Identify terms that are 'rare'</strong></p> <p>Any disease term in Mondo is considered rare if the term, or its ancestor, has modifier <code>MONDO:0021136 'Rare'</code> in the ontology.</p> <p>There are <code>12914</code> Mondo rare disease terms.</p> <p><strong>4. Consider terms in 'gard_rare' subset</strong></p> <p>There are <code>3176</code> Mondo disease terms that are in <code>gard_rare</code> subset which contains Mondo terms that are yet to be treated as 'rare'.</p> <p>We add these terms to our set of Mondo rare disease terms.</p> <p>This increases the Mondo rare disease term count to <code>13866</code>.</p> <p>But for this analysis, we are interested in terms that are both rare and are leaf nodes in the ontology.</p> <p>After considering only leaf nodes, we get <code>10394</code> as the final count of Mondo rare disease terms.</p> <p> </p> <p>Results</p> <p>all-mondo-disease-terms.tsv: As part of our analysis, we generated a TSV containing 21633 Mondo disease terms, each with annotations that signifies whether the term is a rare disease term and whether that term is a leaf node in the ontology.</p>
Rare type III responses: data & data methods (v1.0.0)
<p>This repository includes the data (data-rare-type3-responses.csv) for Kalinkat et al. (2023).</p> <p>The data comprises a literature review on type III functional responses between 2002 and 2022 with 12 variables and 107 observations. Please read the accompanying document (Rall_et_al_2023_Zenodo_Rare-type3-responses_data_methods_v1_0_0.pdf) for the methods and a description of the variables. </p> <p><strong>Reference</strong></p> <p>Kalinkat, G. <em>et al.</em> (2023) ‘Empirical evidence of type III functional responses and why it remains rare’, <em>Frontiers in Ecology and Evolution</em>, 11:1033818. Available at: https://doi.org/10.3389/fevo.2023.1033818.</p>
Whole-brain background-suppressed pCASL MRI with 1D-accelerated 3D RARE Stack-Of-Spirals Readout- Dataset 2
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Whole-brain background-suppressed pCASL MRI with 1D-accelerated 3D RARE Stack-Of-Spirals Readout- Dataset 3
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Rare earth-free motor designs for e-mobility
<p>First webinar of the ReFreeDrive's webinar series. This webinar gives an overview of the different motor technologies that will be developed during the project.</p> <p>The webinar is also available on Youtube. Link: <a href="https://www.youtube.com/watch?v=PziGDLfE5_w">https://www.youtube.com/watch?v=PziGDLfE5_w</a></p>
Spectral library of laser-induced fluorescence (LiF) properties from Smithsonian rare-earth element (REE) orthophosphate standards
<p>The spectral library presents a data set of laser-induced fluorescence (LiF) spectra from rare-earth element (REE) orthophosphates provided and distributed as reference material for microbeam analysis by the Smithsonian National Museum of Natural History (sample IDs: 16484 - NMNH 168499; Jarosewich and Boatner, 1991; Donovan et al., 2002 and 2003). The data set delivers high-resolution LiF spectra excited at three standard laser wavelengths (325 nm, 442 nm, 532 nm) recorded in the UV-visible to near-infrared spectral range (340 - 1080nm). Presented LiF spectra represent data from efficient signal excitation conditions and contain the diagnostic emission lines of individual REE including detailed information on splitting into sub-levels. The LiF spectral library data provides a reference for various applications in spectroscopy-based material composition analysis with the scope of REE identification. LiF as a tool can complement the merging technique of reflectance spectroscopy, because LiF is a particularly well suited method for REE detection and can be used to cross-validate results (e.g. Lorenz et al. 2019) The LiF library allows for transparent and reproducible result analysis in scientific studies and promotes further developments of efficient automated algorithms for REE identification and characterisation. This addresses especially the need for innovative, non-invasive techniques of raw material exploration (securing REE supply) and material stream characterisation (e.g. in e-waste recycling) or for manifold applications in other fields of geosciences (e.g. geology) and physics.</p> <p>references:</p> <p>Donovan, J., Hanchar, J., Picolli, P., Schrier, M., Boatner, L., Jarosewich, E., 2002. Contamination in the rare-earth element orthophosphate reference sam- ples. J. Res. National Institute of Standards and Technology 106, 693–701. doi:10.6028/jres.107.056. </p> <p>Donovan, J., Hanchar, J., Piccoli, P., Schrier, M., Boatner, L., Jarosewich, E., 2003. A reexamination of the rare-earth element orthophosphate reference samples for electron microprobe analysis. Canadian Mineralogist 41, 221– 232. doi:10.2113/gscanmin.41.1.221. </p> <p>Jarosewich, E., Boatner, L., 1991. Rare-earth element reference samples for electron microprobe analysis. Geostandards Newsletter 15, 397–399. doi:10. 1111/j.1751-908X.1991.tb00115.x. </p> <p>Lorenz, S., Beyer, J., Fuchs, M., Seidel, P., Turner, D., Heitmann, J., Gloaguen, R., 2019. The Potential of Reflectance and Laser Induced Luminescence Spectroscopy for Near-Field Rare Earth Element Detection in Mineral Ex- ploration. Remote Sensing 11, 21. doi:10.3390/rs11010021.</p>
Basis sets for the 1s2 ground states of two-electron rare gas ions
<p>This file contains the exponents of Gaussian basis functions optimized in the Dirac-Coulomb approximation for the two-electron ions of the rare gases, He, Ne, Ar, Kr, Rn, and Og. The basis sets are of double-zeta (2z) to septuple-zeta (7z) quality, and include correlating sets:1p (2z), 2p1d (3z), 3p2d1f (4z), 4p3d2f1g (5g), 5p4d3f2g1h (6z), and 6p5d4f3g2h1i (7z). The basis sets are included with the DIRAC program.</p>
Online Resources for Strullu-Derrien et al - The 330–320 Million-Year-Old Tranchée des Malécots (Chaudefonds-sur-Layon, South of the Armorican Massif, France): a Rare Geoheritage Site Containing In Situ Palaeobotanical Remains
<p>This repository contains the following files associate with "The 330–320 Million-Year-Old Tranchée des Malécots (Chaudefonds-sur-Layon, South of the Armorican Massif, France): a Rare Geoheritage Site Containing In Situ Palaeobotanical Remains" by Christine Strullu-Derrien, Alan RT Spencer, Christopher J Cleal and Victor O. Leshyk.</p> <p><strong>Online Resource 1</strong> Model data as a .zip archive (301.5MB) containing .obj/.mtl and texture files for each 3D reconstruction (Models #1-4, whole site reconstruction, detailed reconstruction of the trench, and model of the mine site).</p> <p><strong>Online Resource 2</strong> Video animation showing whole site 3D model (.mp4 | 37.7MB), with quick fly-through of the Tranchée des Malécots showing exposed rock and bedding of the SW wall.</p> <p><strong>Online Resource 3</strong> Video animation showing 3D Model #1 (.mp4 | 35.1MB).</p> <p><strong>Online Resource 4</strong> Video animation showing 3D Model #2 (.mp4 | 83.5MB).</p> <p><strong>Online Resource 5</strong> Video animation showing 3D Model #3 (.mp4 | 45.3MB).</p> <p><strong>Online Resource 6</strong> Video animation showing 3D Model #4 (.mp4 | 65.8MB).</p> <p><strong>Online Resource 7</strong> Video animation showing 3D model of the Malécots mine headframe (.mp4 | 14.9.0MB).</p>
Summary statistics for "Exome sequencing identifies rare damaging variants in ATP8B4 and ABCA1 as risk factors for Alzheimer's Disease"
<p>These are the burden test results (summary statistics) for the publication:</p> <p>"Exome sequencing identifies rare damaging variants in ATP8B4 and ABCA1 as risk factors for Alzheimer’s Disease",</p> <p>Nature Genetics, 2022.</p> <p> </p> <p><em>Format: tab-separated-value.</em></p> <p><em>Fields:</em></p> <ul> <li><em>gene_stable_id: Ensembl gene id</em></li> <li><em>gene_name: standard gene name</em></li> <li><em>pvalue: burden test significance (likelihood ratio test, population structure correction based on 6 PCA components)</em></li> <li><em>cmac_all: sum of minor allele dosages across all contributing samples and variants</em></li> <li><em>group: variant group (LOF, LOF+REVEL>=75, LOF+REVEL>=50, LOF+REVEL>=25, see publication methods for further selection criteria).</em></li> <li><em>beta/se: beta/se of logistic ordinal regression (see publication methods). Positive = risk-increasing. Negative = risk-decreasing.</em></li> </ul> <p> </p>
Interviews for New Business Models for Pharmaceutical Innovation and Access to Medicines - Rare Diseases
<p>These supplementary materials represent the partial dataset in the form of semi-structured interviews, collected and analyzed in the research article "Alternative innovation models of pharmaceutical development for rare disease drugs: how (and) do they work?: A qualitative study". This article is one of the outcomes of the "New Business Models for Pharmaceutical Innovation and Global Access to Medicines" research project, conducted at the Global Health Center, within the Geneva Graduate Institute. The dataset contains 10/11 interviews collected and used in this article, which are published with the informed consent of the interviewees.</p> <p>Details about the research project can be found at: <a href="https://www.graduateinstitute.ch/NBM">https://www.graduateinstitute.ch/NBM</a></p>
Data for: Systematic and highly resolved modelling of biodiversity in inherently rare groundwater amphipods (Journal of Biogeography, 2024)
<p>Original research article:</p> <p>Knüsel, M., Alther, R., Locher, N., Ozgul, A., Fišer, C. & Altermatt, F. (2024). Systematic and highly resolved modelling of biodiversity in inherently rare groundwater amphipods. <em>Journal of Biogeography</em>, https://doi.org/10.1111/jbi.14975.</p>
Data of publication All-optical control of long-lived nuclear spins in rare-earth doped nanoparticles
<p>Data corresponding to the figures of the publication "All-optical control of long-lived nuclear spins in rare-earth doped nanoparticles" by D. Serrano et al. (https://www.nature.com/articles/s41467-018-04509-w). A text file describes data in each compressed folder, please refer to the publication for more details. </p>
Data of publication Controlled size reduction of rare earth doped nanoparticles for optical quantum technologies
<p>Data corresponding to the figures of the publication " Controlled size reduction of rare earth doped nanoparticles for optical quantum technologies" by S. Liu et al. (https://pubs.rsc.org/en/content/articlelanding/2018/ra/c8ra07246a#!divAbstract). A text file describes data in each compressed folder, please refer to the publication for more details. </p>
CellSIUS provides sensitive and specific detection of rare cell populations from complex single cell RNA-seq data: Codes and processed data
<p>Codes and processed data to reproduce the analysis discussed in: </p> <p>Wegmann <em>et Al.</em>,<strong> CellSIUS provides sensitive and specific detection of rare cell<br> populations from complex single cell RNA-seq data</strong>, Genome Biology 2019 (Accepted)<br> </p>
Data of the publication Rare Earth‐Diamond Hybrid Structures for Optical Quantum Technologies
<p>Data of the publication published under the reference: I.G. Balașa et al., Advanced Optical Materials, 2401487 (2024).</p>
The mycobiome of the gut of willow wood borer, Xiphydria prolongata (Hymenoptera: Xiphydriidae): a rich source of rare yeasts
<p>A high-throughput amplicon sequencing as a culture-independent approach was used to identify the gut mycobiome of the willow wood borer <em>Xiphydria prolongata</em>. The findings of this study are significance in terms of the insect-fungal interactions and indicate the unexpected richness of the mycobiome and the presence of many rare yeast species in the wood borer gut. A total of 40 fungal genera were found, and among them, only one endophytic fungi, <em>Daldinia</em> (Hypoxylaceae), has been previously reported in <em>Xiphydria.</em> <em>Zygosaccharomyces siamensis</em> is the most prevalent ascomycete species, while <em>Rhodosporidiobolus colostri</em> is the most abundant basidiomycetous yeast in <em>X. prolongata</em>. Some of the species identified in here was known as very rare fungus such as <em>Skoua fertilis</em>, <em>Chaetomium nepalense, R. colostri </em>and<em> Vustinia terrae</em>. This study is also the first report to <em>S. fertilis </em>and<em> V. terrae</em> in the insect gut flora. These funguses most likely aid in the digestion of lignocellulose in the gut of wood borer. Therefore, further researches are required to know the source of acquisition and functional role of these yeast and their industrial potential.</p>
Data For: Identifying rare variants inconsistent with identity-by-descent in population-scale whole-genome sequencing data
<p>Simulation output and Genome-wide scan for nIBD variants in UK10K data as reported in:</p> <p>Identifying rare variants inconsistent with identity-by-descent in population-scale whole-genome sequencing data</p> <p>Johnson KE, Adams CJ, Voight BF. Methods Ecol Evol 2022 Nov;13(11): 2429–2442.</p> <p>Code available at: https://github.com/kelsj/EVICORD</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.